Variant report

Variant	rs412328
Chromosome Location	chr1:86266842-86266843
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs186376	0.83[CEU][hapmap]
rs193398	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1977331	0.95[CHB][hapmap]
rs313710	0.91[CHB][hapmap]
rs313712	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs313715	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs313719	0.83[CHB][hapmap]
rs313732	0.90[CHB][hapmap]
rs313733	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs313734	0.91[CHB][hapmap]
rs313735	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs313758	0.83[CEU][hapmap]
rs313759	0.83[CEU][hapmap]
rs366187	0.91[CHB][hapmap]
rs380654	0.91[CHB][hapmap]
rs432168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs449901	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs486417	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs598104	0.91[CHB][hapmap]
rs673506	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv817212	chr1:86127851-86658426	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv546721	chr1:86226352-86392577	Weak transcription Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv999743	chr1:86241246-86364846	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs412328	LRP10	trans	parietal	SCAN
rs412328	ANKS6	trans	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86257200-86274000	Weak transcription	Fetal Lung	lung
2	chr1:86262800-86268600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:86263400-86272200	Weak transcription	GM12878-XiMat	blood
4	chr1:86264600-86272600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr1:86264800-86267600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr1:86265800-86272400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:86266200-86267200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:86266200-86267600	Enhancers	NHDF-Ad	bronchial
9	chr1:86266800-86267400	Strong transcription	Primary hematopoietic stem cells	blood
10	chr1:86266800-86267600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:86266800-86268000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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